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Genome wide DNA Copy Number Analysis of high hyperdiploid acute lymphoblastic leukemia

ABSTRACT: This dataset included samples with high hyperdiploid acute lymphoblastic leukemia (ALL) that were collected from four different cohorts: the Division of Clinical Genetics, Lund University, Sweden. All samples were genotyped using Affymetrix SNP Array or Illumina's BeadArray platform. This dataset has been used for copy number aberrations analysis for high hyperdiploid ALL.

PROVIDER: EGAS00001007049 | EGA |

REPOSITORIES: EGA

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Integrated analysis of genome-wide copy number and matched expression data reveals novel genes in esophageal adenocarcinoma

Project description:The incidence of esophageal and junctional adenocarcinoma has increased 6-fold in the west in the last 30 years and 5 year survival remains <14%. We aimed to characterize genome-wide aberrations in esophageal adenocarcinoma to further understand disease pathogenesis and ultimately identify groups with differential survivals with implications for clinical management. Oligo-array-based high-resolution analysis of copy number changes in 89 fresh frozen esophageal adenocarcinoma resection sections with long-term clinical follow-up data was performed. Good quality array comparative genomic hybridization profiles were obtained from 56/89 of the samples (63%). Our analyses confirmed known genomic aberrations in esophageal adenocarcinoma and identified 3 novel genomic regions with copy number changes. A modified T test with adjusted Bonferroni correction identified 17 genes with significantly different log2 ratios (p<4x10-7), including 6 novel genes, that characterize a group with a poorer survival. Total DNA isolated from human tissue sections was used to make fluorescently labeled DNA that was hybridized to Illumina HumanCytoSNP-12 Beadarray. All protocols were carried out following Illumina's standard protocols. After hybridization, raw data were recorded and normalized using Illumina's BeadStudio software v2.0. Matched expression data: GSE25201 GSE19417 D2 MRC/OEA0022CJ5 (GSM482819) D3 MRC/OEA0032CJ5 (GSM482817) D27 MRC/OEA0272CJ1 (GSM482814) D36 MRC/OEA0362CJ3 (GSM482806) D37 MRC/OEA0372AJ0 (GSM482800) D96 MRC/OEA0962BJ0 (GSM482847) D118 MRC/OEA1172CJ1 (GSM482848) D138 MRC/OEA1382CJ0 (GSM482844) D156 MRC/OEA1562CJ2 (GSM482853)

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Sister chromatid cohesion defects are associated with chromosomal copy number heterogeneity in high hyperdiploid childhood acute lymphoblastic leukemia.

Project description:High hyperdiploid acute lymphoblastic leukemia (ALL) is one of the most common malignancies in children. The main driver event of this disease is a nonrandom aneuploidy consisting of gains of whole chromosomes but without overt evidence of chromosomal instability (CIN). Here, we investigated the frequency and severity of defective sister chromatid cohesion-a phenomenon related to CIN-in primary pediatric ALL. We found that a large proportion (86%) of hyperdiploid cases displayed aberrant cohesion, frequently severe, to compare with 49% of ETV6/RUNX1-positive ALL, which mostly displayed mild defects. In hyperdiploid ALL, cohesion defects were associated with increased chromosomal copy number heterogeneity, which could indicate increased CIN. Furthermore, cohesion defects correlated with RAD21 and NCAPG mRNA expression, suggesting a link to reduced cohesin and condensin levels in hyperdiploid ALL. Knockdown of RAD21 in an ALL cell line led to sister chromatid cohesion defects, aberrant mitoses, and increased heterogeneity in chromosomal copy numbers, similar to what was seen in primary hyperdiploid ALL. In summary, our study shows that aberrant sister chromatid cohesion is frequent but heterogeneous in pediatric high hyperdiploid ALL, ranging from mild to very severe defects, and possibly due to low cohesin or condensin levels. Cases with high levels of aberrant chromosome cohesion displayed increased chromosomal copy number heterogeneity, possibly indicative of increased CIN. These abnormalities may play a role in the clonal evolution of hyperdiploid pediatric ALL.

| S-EPMC8247877 | biostudies-literature

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